gather_coords Subroutine

subroutine gather_coords(this, frag_code)

    class(mimic_communicator), intent(inout) :: this
    !> subsystem_type belonging to each code
    type(subsystem_type), dimension(:), intent(in) :: frag_code

    real(kind=dp), dimension(:), allocatable, target :: coordinates
    type(fragment_type) :: current_fragment
    integer :: code_atoms

    integer :: n_code, n_fragment, n_atom, n_map
    integer :: offset, location
    logical :: overlapped = .false.

    do n_code = 1, this%num_clients
        code_atoms = frag_code(n_code)%num_atoms

        allocate(coordinates(code_atoms * 3))
        call this%send_command(MCL_SEND_ATOM_COORDS, n_code)
        call mcl_receive(coordinates, code_atoms * 3, MCL_DATA, n_code)
        offset = 0
        do n_fragment = 1, size(frag_code(n_code)%fragments)
            current_fragment = frag_code(n_code)%fragments(n_fragment)
            do n_atom = 1, current_fragment%num_atoms
                location = (current_fragment%atoms(n_atom)%id - 1) * 3 + 1

                do n_map = 1, size(this%overlap_maps(n_code)%maps)
                    if (this%overlap_maps(n_code)%maps(n_map)%id == &
                             current_fragment%atoms(n_atom)%id) then
                        overlapped = .true.
                        exit
                    end if
                end do ! n_map

                if (overlapped) then
                    overlapped = .false.
                    ! offset = offset + 3
                    cycle
                end if

                current_fragment%atoms(n_atom)%coordinate = coordinates(location : location + 2)
            end do ! n_atom
            offset = offset + current_fragment%num_atoms * 3
        end do ! n_fragment
        deallocate(coordinates)
    end do ! n_code

end subroutine gather_coords